Download Welcome Letter ytoscape

May 27, 2014
Welcome
Summary
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Cytoscape v3.1.1 is now available for immediate download.
It addresses 46 issues relative to v3.1:
o Several small issues with new filter facility, including reverting topology filers to
pre-v3.1 behavior
o Improved network and attribute imports for Excel, CSV, and TXT files
o Occasional hangs during startup, shutdown, circular layout, and session load
o Better user and App Developer documentation
o Feature improvements for exporting networks to web pages
9 more Apps are available in the App Store as compared to the v3.1 release.
It is ready for use by all segments of the Cytoscape community.
It continues v3.1’s core feature set, specifically:
o It is upward compatible and can coexist with previous Cytoscape versions
o The most popular plugins from previous versions are available, with more to
follow.
What to do next …
Release notes: http://www.cytoscape.org/releasenotes.html
Dear Cytoscape User
We are proud and pleased to release Cytoscape v3.1. This new release contains both new features and
improvements to functionality and documentation, all of which are described in Section 11.
Additionally, v3.1, 11 Apps were added to the App Store, bringing the total to 53. The new ones include:
AllegroLayout
BridgeDB
chemViz2
clusterMaker2
Cyrface
CytoCopteR
KDDN
Rene
setsApp
Variation
WormPlot
If you are a new or casual Cytoscape user, welcome aboard! Feel free to either read on
or jump ahead to What to Do Next for a quick start.
For clarity, references to “Cytoscape 3.x” apply to all Cytoscape versions 3.0.0 and later.
For Cytoscape v2.x Users
Previous Cytoscape releases (through v2.8.3) focused on adding numerous annotation, import, layout,
analysis, and visualization features, all of which have combined to deliver critical insights into biological
processes of interest to Cytoscape’s broad and loyal user community. In fact, many of these features
were created and contributed by Cytoscape users, themselves, using Cytoscape’s plugin architecture.
Version 3.0 marked a major reorganization of Cytoscape program code – it enabled us to deliver
additional features more quickly and reliably than before, including improvements that benefit new
users, casual users, power users, and app developers. Along the way, some features were changed to
allow them to better interoperate with other features, some little-used features were dropped, and user
interface was improved. We were particularly excited about the new Cytoscape App Store (described
below), which afforded users access to the growing collection of apps (formerly called plugins) produced
by fellow Cytoscape users. A table of new features is presented in Section 7.
Since v3.0, we released updates v3.0.1 and v3.0.2 as maintenance releases, and then v3.1 as a feature
release, including greatly improved visual styles, node filtering, and web publishing.
While all version 3 releases are upwardly compatible with previous Cytoscape versions (i.e., they can
load, analyze, and display networks and attributes stored using previous versions, including v2.x), they
can coexist with previous versions on the same workstation. It is not necessary to uninstall previous
versions before installing a version 3 release, and you can choose to use both on the same workstation.
Version 3 is still a work in progress and continues to mature due to the outstanding efforts of its vibrant
worldwide development community. Notably, while the Cytoscape team has ported the most popular
plugins (as apps) from previous versions, porting less popular plugins was deferred so as to deliver
version 3 sooner and with features that support cutting edge investigation. A table of apps and their
status is presented in Section 8.
Finally, we recognize that with all new software (including version 3), there are growing pains. While we
hope our users will learn to love v3’s new features, users may also expect to relearn rationalized
features and occasionally uncover a bug. With version 3.0, we are rolled out new manuals, tutorials,
web pages, and support channels that we hope can create and maintain highly productive experiences
for all types of Cytoscape users. We continue to improve these materials monthly. A table describing
Cytoscape support is presented in Section 9.
We are very excited to make this release, and hope you find it an indispensable tool in your research. To
get you started, we have provided additional introductory material to get you started on the right foot,
and we have also provided background material for general interest.
Please let us know how we’re doing and how we can better advance your research!
The Cytoscape Team
What to Do Next
We hope to help you use Cytoscape in the most productive way. Your next steps depend on how
experienced you are with Cytoscape and what you would like to do. In the table below, please find the
category that best describes you, and proceed accordingly.
Type of Cytoscape User
New
Casual
Power
App Developers
General Interest
Where to Read Next
For New Users (Section 1)
For Casual Users (Section 2)
For Power Users (Section 3)
For App Developers (Section 4)
Try getting oriented by reading:
General Background (Section 5)
Cytoscape App Store (Section 6)
Then try browsing:
New Features (Section 7)
App Status (Section 8)
Support Offering (Section 9)
Future Plans (Section 10)
To get your feet wet, try:
For New Users (Section 1)
1. For New Cytoscape Users
What is Cytoscape?
Cytoscape is software that can help you visualize complex networks (as graphs) representing
relationships between genes, proteins, or other entities. Cytoscape tracks and displays these entities (as
graph nodes) and relationships between them (as graph edges). Cytoscape, per se, does not assign
meaning to either nodes or edges – you can assign your own meanings to them, and you can add your
own node or edge attributes (e.g., name, measurements, states, etc.) that customize your graph to
represent semantics important to you. While Cytoscape provides simple analytics and visualizations,
others are available as apps from the Cytoscape App store (see Section 6).
What Do I Need Before I Can Use Cytoscape?
At the very least, you must provide Cytoscape with a list of nodes. You can also provide a list of edges
and attributes. You can enter your graph manually or import it from your own files – Cytoscape supports
a wide variety of file formats, including text and Excel. Cytoscape can also load pre-configured networks
(e.g., from BioGRID) so you can leverage them without having to enter them yourself.
Can Cytoscape Help Me Get Started?
Yes! The Cytoscape team had provided many resources tailored for all kinds of users (see Section 9). To
start, there is an Installation Guide and numerous tutorials. Once you load your graph, you may find
additional useful analytics and visualizations at the App Store (see Section 6).
Which Cytoscape Version Should I Use?
Generally, you should use v3.1.1 (the newest version). v2.x has been in the field for several years and
will be supported into the future, but over time, v3.x and successors will be better supported.
Note that if you have already installed v3.0.0, v3.0.1, v3.0.2, or 3.1, you can install v3.1.1 without
uninstalling your previous version.
How to Download and Install v3.x
 Surf to http://www.cytoscape.org, click on the Download Cytoscape button, and follow the
prompts
 Be sure to consult with the Release Notes (viewable via the Release Notes button) for issues
and solutions pertaining to your installation
 Surf to http://www.cytoscape.org, click on the Release Notes button, click on a User Manual
link, and follow the instructions in the Launching Cytoscape section.
2. For Casual Cytoscape Users
If you’re confident of your Cytoscape skills, please read the Power Users information (Section 3).
If you’re Cytoscape skills are rusty, please continue with the New Users information (Section 1).
3. For Cytoscape Power Users
Is v3.x for Me?
The answer is most likely yes, provided you use the apps (formerly known as plugins) available for v3.x –
apps are available from the new Cytoscape App Store, which you can browse directly (Section 6). Note
that some v2.x apps have been incorporated directly into Cytoscape and need not be downloaded or
installed. Consult the Apps Status table (Section 8) to see a list of these apps.
Note that v2.x plugins are not compatible with v3.x apps, and vice versa. If you rely on v2.x plugins that
are not yet available for v3.x, you may need to remain with v2.x instead of upgrading to v3.x. Note, also,
that the Cytoscape community is converting v2.x plugins to v3.x apps -- you might occasionally revisit the
App Store to see if an app you need becomes available.
What’s New in v3.x?
As described in the Welcome letter (above), v3.x incorporates a number of new features (Section 7) and
productivity enhancing support offerings (Section 9), including the Cytoscape App Store (Section 6). The
General Background section (Section 5) describes the rationale, advantages, and issues with v3.x.
Will Support for v2.x Continue?
Cytoscape v2.x will be supported by the Cytoscape community for now, but with fewer upgrades and
support options over time.
Can I use v2.x and v3.x at the Same Time?
You can experiment with v3.x by installing it on your workstation – you can use both v2.x and v3.x on
the same workstation.
How to Prepare for v3.x
1. If you have already installed a v3.1.1 beta version, please uninstall it before proceeding. The
Cytoscape v3.0 and v3.1x versions can coexist with v3.1.1, and do not need to be uninstalled.
2. Consult the Apps Status table (Section 8) to verify that the apps you need are available. Some
apps have become part of the Cytoscape core, and you won’t need to download them. Other
apps are available in the Cytoscape App store (described in Section 6).
3. Browse the New Features table (Section 7) to see what we have added since v2.x.
4. Browse the Future Plans table (Section 10) and Support Offering table (Section 9) to see where
the Cytoscape community is going.
How to Download and Install v3.x
 Surf to http://www.cytoscape.org, click on the Download Cytoscape button, and follow the
prompts
 Be sure to consult with the Release Notes (viewable via the Release Notes button) for issues
and solutions pertaining to your installation
 Surf to http://www.cytoscape.org, click on the Release Notes button, click on a User Manual
link, and follow the instructions in the Launching Cytoscape section.
4. For Cytoscape App Developers
Cytoscape manages graph storage and display, and contains a number of common analytic and
visualization functions. App Developers may write apps (formerly known as plugins) to perform
problem-specific analytics, graph layouts, or other visualizations.
Before starting app development, you should be familiar with overall Cytoscape usage and functionality
– see the Power Users section (Section 3) to start working with v3.x if you have not already done so.
Note that v2.x plugins do not work with v3.x. In order get the benefits of improved stability, the
Cytoscape team found it necessary to change the relationship between plugins/apps and the Cytoscape
core. Many plugins have been ported to v3.x (see Section 8). The porting exercise is substantial, and
once a plugin is converted to an app, it will continue to work at least until v4.0 is released – there is no
v4.0 planned at this time. For more on this topic, see:
http://wiki.cytoscape.org/Cytoscape_3/CoreDevelopment/Motivation
Should I Convert My v2.x Plugin to a v3.x App?
Yes! Cytoscape v2.x will be supported by the Cytoscape community for now, but with fewer upgrades
and support options over time.
How Do I Get Started With App Development?
To get started with app development:
http://wiki.cytoscape.org/Cytoscape_3/AppDeveloper
To convert a v2.0 plugin to a v3.x app, refer to:
http://wiki.cytoscape.org/Cytoscape_3/AppDeveloper/PluginPortingGuide
For a broader view of the Cytoscape system (including the Core), refer to:
http://wiki.cytoscape.org/Cytoscape_3/CoreDevelopment
Are there App Samples?
Yes! See:
http://opentutorials.cgl.ucsf.edu/index.php/Tutorial:Creating_a_Simple_Cytoscape_3_App
Also note the App Cookbook:
http://wiki.cytoscape.org/Cytoscape_3/AppDeveloper/Cytoscape_3_App_Cookbook
5. General Background
The overall mission of Cytoscape is to be a freely available worldwide asset supporting network analysis
and visualization for systems biology science.
The major focus of v3.x is the modularization and rationalization of code to solve stability issues in v2.x
encountered as multiple developers pursued multiple agendas. Under v2.x, internal programmatic
interfaces evolved from one release to the next, leading to the failure of working plugins over time and
negative interactions between otherwise working plugins. Ultimately, this resulted in loss of
programmer and user productivity, and undermined community confidence in Cytoscape.
v3.x addresses these issues by adopting modular coding practices promoted by the OSGi architectural
framework1. This enables both the Cytoscape core and externally developed apps (formerly called
plugins) to evolve independently without compromising unrelated functionality. At the logical level,
Cytoscape leverages OSGi precepts to produce v3.x APIs having cleaner and clearer demarcations
between functional areas. At the deployment level, OSGi enables on-the-fly substitution of one
processing element for another (e.g., apps) in order to tailor Cytoscape to meet user requirements at
runtime without reinstalling or reconfiguring Cytoscape.
Creating v3.x occupied an international team of engineers for over a year, and represents a strong
investment toward reducing future development and support costs, and increasing reliability and
evolvability. With the completion of v3.x, we expect to leverage v3.x as a platform to satisfy the evolving
needs of multiple stakeholder groups, and as a platform enabling research on leading edge analysis and
visualization techniques. v3.x is the intended successor to v2.x, with development and support of v2.x
expected to diminish and disappear over time in favor of v3.x.
We believe that users will benefit most directly from the v3.x by:
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experiencing fewer core and app bugs from one release to the next
the availability of more and richer apps (due to developers spending less time tracking and fixing
bugs)
more core features with higher biological and logistical value (due to improved flexibility
provided by interface-driven development)
During the creation of v3.x, a number of features were added, as listed in the New Feature Table below.
As a result, we incurred a number of current and future costs:
Cost
Slower startup time
Loss of plugins
1
Reason
OSGi module inventorying
Lag in upgrading less popular
plugins
Time frame for addressing
near-to-medium term
as needed
www.osgi.org – also used as the basic framework for Eclipse and numerous commercial products
6. The Cytoscape App Store
The Cytoscape App Store is new in v3.x and targets broad demographics through specific features:
Cytoscape User
New or Casual
Power or Frequent
Plugin Developers
Benefit
Find Cytoscape functionality easier via familiar
paradigms of search and tag navigation
Find and install apps easier and provide
crowdsourced rating and reviews
Have a dedicated presence for their work, including a
direct line to their users and critical statistics to
justify their development on the Cytoscape platform.
Furthermore, the App Store supports contests and social incentives that encourage critical technical and
community development, including porting, analytics, rating/reviewing, and so on.
Note that the App Store supports only Cytoscape v3.x and does not contain plugins compatible with
earlier Cytoscape versions. Likewise, plugins that work with earlier versions are not compatible with v3.x
– Section 8 contains a list of apps available for v3.x.
To access the App Store, access Cytoscape’s new Apps menu and choose the App Manager menu item,
or use your browser to surf directly:
http://apps.cytoscape.org
7. New Feature Table
Feature
Welcome screen
Beneficiary
New users (for solicitousness), casual
and power users (for convenience)
All users
Manual Section
5.1. Welcome Screen
23. Cytoscape.js and
Cytoscape
17.2. Merging Tables
24. Scripting
New filter facility
Power users wanting to present
networks on web pages
Users of attributes in multiple tables
Power users creating repeatable
workflows
Power users using other applications
to communicate with Cytoscape
All users
Group annotations
Automatic citations
Improved PSICQUIC
access
Users with highly annotated networks
Users publishing Cytoscape analyses
5.3.8 Help
All users needing to download
protein databases
New Style replaces
VizMapper
Export to cytoscape.js
Merge columns
Command line interface
REST interface
14. Styles
12. Finding and Filtering
Nodes and Edges
8. App Status Table
For the most up to date list of apps, see the App Store (described in Section 6). A URL for our
development list is shown below, as a list of apps and their status at the time this letter was authored.
https://docs.google.com/spreadsheet/ccc?key=0ArzUWDuvdBndDI0R0kwOERjN1ZhcDZseC00dVZNNlE&authkey=CMGe99EM#gid=0
Apps new since the v3.1 release are highlighted in yellow.
App
addParentNeighbors
AdvancednetworkMerge
AgilentLiteratureSearch
AllegroLayout
AllegroMCODE
APCluster
APID2NET
bayelviraApp
BiLayout
BiNGO
bioCycPlugin
BiogridPlugin
BiomartClient
BioNetBuilder
Capability
For a selected node in child network, adds
neighboring nodes from a parent network .
Merges multiple networks.
Mines scientific literatures to find ones
related to search term and to create
interaction network based on the search
result.
High-speed and high-quality layout app
designed for large-scale networks
Very fast clustering based on MCODE
algorithm.
Uses affinity propagation described in Frey
BJ and Duec D (2007) to perform clustering.
Downloads PPI data from
http://bioinfow.dep.usal.es/apid/ and
performs various analyses including protein
motif, GO, hub identification, etc. through
the original GUI. Equipped with impressing
"rainbow" coloring of nodes.
Builds Bayesian networks using a file of
patterns as input data using Naive Bayes,
Semi Naive Bayes, Selective Naive Bayes,
TAN, KDB and Class Tree Naïve algorithms.
Finds a bipartite network for two sets of
user-selected nodes and performs layout.
Calculates overrepresented GO terms in
the network and display them as a network
of significant GO terms.
Loads any pathway in bioCyc database.
Original panel provides useful information
for each node.
Loads Biogrid tab file onto Cytoscape.
Retrieves attributes associated with given
gene or protein
Through the wizard, user can easily
construct networks from public databases.
User can also create interologs.
Status
Available in App
Store
Available in App
Store
Available in App
Store
Available in App
Store
In Progress
BioQualiPlugin
Bisogenet
BLAST2similarityGraph
BridgeDB
CABIN
CalculatenodeDegree
CentiScaPe
ChemViz
ClojureEngine
ClueGO
CluePedia
clusterExplorerPlugin
clusterMaker2
ClusterONE
ClusterViz
commandTool
CommFinder
Commonattributes
CoNet
Performs consistency check of regulatory
network and expression data.
Retrieves interactions associated with input
IDs. Sophisticated UI gives links to GO,
KEGG, etc.
Visualizes BLAST similarity as graph.
Performs identifier mapping services based
on various resources
Integrates interaction datasets from
different resources to explore the
integrated network and to perform
confidence analysis for interactions. User
can give weight to each interaction set
which will be used for the level of
confidence.
Simply calculates degree for selected single
node.
Calculates topological characteristic values
(ex. Centralities) for each node.
Visualizes chemical structure of each
compound in chemical network with
original interface.
Provides Clojure API.
Creates and visualizes a functionally
organized GO term network or pathway
from given interaction network.
Pathway insights using integrated
experimental and in silico data
Explores a given similarity graph.
Clusters densely connected nodes and
node attributes (i.e. expression data) in a
given network. Results of these two types
of clustering can be analysed in the
integrated interface.
Finds overlapping protein complexes in a
protein interaction network. Clusters are
visualized by original interface with their pvalues.
Clustering based on FAG-EC, EAGLE or
MCODE. Found cluster can be subjected to
GO enrichment analysis.
Provides simple command-line interface to
Cytoscape.
Clustering based on QCUT, HQCUT, MCL,
MCODE.
Find attributes shared between selected
nodes.
Clustering based on FAG-EC, EAGLE or
MCODE. Found cluster can be subjected to
GO enrichment analysis.
Available in App
Store
Available in App
Store
Available in App
Store
Available in App
Store
Available in App
Store
Available in App
Store
Available in App
Store
Available in App
Store
Available in App
Store
ConsensusPathDBplugin
Cy3 Performance Reporter
CyAnimator
CyClus3D
CyGoose
CyKEGGParser
Cyni Toolbox
CyOog
CyPath2
Cyrface
CyTargetLinker
CyThesaurus-ID-Mapping
CytoCluster
CytoCopteR
cytoHubba
CytoKegg
CytoNCA
Cytoprophet
CytoSaddleSum
CytoscapeRPC
Retrieves interaction evidences for given
pair of genes or proteins
Collects information about Cytoscape 3
performance
Creates animation based on added frames
of network views.
Clusters a given network based on threenode motifs. Accepts multiple types of
interactions. Cluster ID is given to edge
attributes, "EdgeCluster".
Provides Gaggle Boss, which routes data
from one application to another.
Parses and increases accuracy and
specificity of KEGG pathways.
Network Inference Toolbox for inferences
from bio-data.
GUI client app for Pathway Commons 2
(BioPAX L3 pathway data) web service.
Establishes an interface between R and
Cytoscape by using different Java-R
libraries
Extends biological networks with
regulatory interactions.
Performs ID mapping using BridgeDb and
other public or custom database sources.
Analyze and visualize clusters from
network.
Friendly way to use CellNOptR taking
advantage of the network visualization and
analysis of Cytoscape and without
requiring knowledge on R
Predicts and explores important nodes and
subnetworks in a given network by several
topological algorithms.
Identify Kegg pathways associated to
specific expression profiles.
Providing calculation, evaluation and
visualization analysis for several
centralities of weighted and unweighted
network.
Finds enriched function based on sum-ofweight scores.
Allows user to query and modify networks
through an XML-RPC connection.
Available in App
Store
Available in App
Store
Available in App
Store
Available in App
Store
Available in App
Store
Available in App
Store
Available in App
Store
Available in App
Store
Available in App
Store
Available in App
Store
CytoSEED
CytoSQL
DisGeNET
DomainGraph
DroID
D3.js Exporterer
dynamicXpr
DynNetwork
edgeLengthPlugin
edgeLister
Enhanced Graphics
EnhancedSearch
EnrichmentMap
eXamine
ExprEssence
ExpressionCorrelation
FERN
FluxViz
Enables users to view, manipulate and
analyze metabolic models created by the
Model SEED. The reactions are organized
into a set of maps based on each reaction's
membership in KEGG pathways.
Retrieves attributes from SQL databases by
invoking query command.
Queries and analyzes networks of diseases
and their associated genes.
Visualizes domain-domain interactions
which connect pairs of interacting proteins.
Retrieves interactions associated with input
IDs. Detailed information associated with
interactiong proteins can also be obtained.
Export Cytoscape network and table as
D3.js style JSON
Dynamically change colors of nodes like a
movie according to their expression level
across many conditions.
Visualize dynamic networks.
Calculate edge length in the main network
view window, and stores them as edge
attributes "length".
Records selected edges and provides some
functionality for them (ex. hiding recorded
edges)
Passthrough mapper for charts and
gradients.
Performs keyword search. Wildcards,
logical operators, etc. are allowed.
Visualizes enrichment of specific functions
(GO terms) by interactions between
functions.
Set-oriented visual analysis approach for
annotated modules that displays set
membership as contours on top of a nodelink layout.
Searches for differentially altered links in a
given network using multiple set of
expression data.
Makes a similarity network where nodes are
genes, and edges denote highly correlated
genes.
Performs stochastic simulation of chemical
reaction networks.
Visualizes fluxes as visual effect to edges on
Cytoscape network.
Available in App
Store
Available in App
Store
Available in App
Store
Available as part
of core
Available in App
Store
FM3
FunNetViz
Gasoline
GeneMANIA
GenomeSpace
Genoscape
GFD-Net
GIANT
GoogleChartFunctions
GPML-Plugin
GraphletCounter
GraphMLReader
GroovyEngine
GroovyScriptingEngine
GroupTool
HiderSlider
HyperEdgeEditor
HyperModules
IgraphPlugin
IntActWSClient
Performs one of the fastest multilevel force
directed Layouts called FM3 Layout
introduced by Hachul S et al 2005.
Integrates and visualizes co-expression
network with biological role of transcripts
(e.g., GO terms). Centrality measures are
equipped.
Multiple local alignment of protein-protein
interaction (PPI) networks.
Generates interaction networks from
public databases based on user's list of
genes. Also provides annotation and
putative function for those genes.
Enables communication with
GenomeSpace
Analyze a gene network based on Gene
Ontology (GO) and calculate a quantitative
measure of its functional dissimilarity.
Network analysis according to the
Guimerà-Amaral cartography
Creates image from attribute values (URL)
using the Google Chart API.
Enables import of GPML file via import
menu.
Calculates "graphlet" (small connected nonisomorphic subgraph) degree distribution.
Loads interactions or pathways in GraphML
format.
Provides scripting interface of Groovy.
Provides scripting interface of Groovy.
Enables user to defines groups of nodes. For
each group, basic information such as
number of nodes will be displayed on the
panel.
Provides user sliders which can hide nodes
whose continuous attribute is below
threshold specied by sliders.
Enables one to create hyper-edge by
Cytoscape editor.
Uses local graph search heuristics to detect
closely connected gene network regions in
which gene mutations correlate with
clinical features.
Brings some functionality of Igraph such as
layouts into Cytoscape. Mac only.
Retrieves interactions associated with
input IDs.
Available in App
Store
Available in App
Store
Available in App
Store
Available in App
Store
Available in App
Store
Available as part
of core
In Progress
Available in App
Store
Replaced by
PSICQUIC
Interference
iRefScape
jActiveModules
JavaScriptEngine
JEPETTO
KDDN
KEGGscape
KeyPathwayMiner
KGMLReader
mcl-new
MCODE
MetaNetter
MetanodePlugin2
MetDisease
MetScape
MiMIplugin
Evaluates the topological effects of single or
multiple nodes removal from a network
using the effect to Radiality, Closeness,
Betweenness, Centroid Value and
Eccentricity.
Retrieves interactions associated with input
IDs. Detailed information for each
interaction as well as link to iRefIndex is
provided.
Finds clusters where member nodes show
significant changes in expression levels.
Provides Java Script API.
Performs biological gene sets enrichment
analysis based on interaction network and
topological properties.
Learn biological network topology and its
changes using profiling data and domain
knowledge
Constructs KEGG pathway on Cytoscape3
Detects highly-connected sub-networks
where most genes show similar expression
behavior.
Enables import of KEGG XML file via import
menu.
Clusters given network. Subnetwork is
indicated by set of nodes, and they are
shown by selecting subnetwork number.
Clusters a given network based on vertex
weighting by local neighborhood density
and outward traversal from a locally dense
seed protein to isolate the dense regions.
Infers of metabolic networks based on high
resolution metabolomic data.
Enables user to define "meta-node", a
group of nodes. Meta-nodes can have
hierarchy.
Annotates metabolic networks with MeSH
disease terms and links to references.
Loads human or mouse metabolic network.
Sophisticated GUI is provided which allows
user to perform various tasks including
gene expression analysis along the
pathways.
Retrieves interactions associated with input
IDs. User can add own annotations to genes
which can be viewed by different users.
In Progress
Available in App
Store
Available as part
of core
Available in App
Store
Available in App
Store
Available in App
Store
Available in App
Store
Available in App
Store
Available as part
of core
Available in App
Store
Available in App
Store
In progress
MINE
MiSink
MONET
Mosaic
NamedSelection
NCBIClient
NCBIEntrezgeneUserInterface
NeighborHighlight
NeMo
NetAtlas
NetCirChro
NetMatch
NetworkAnalyzer
NetworkEvolution
nodeCharts
OmicsAnalyzer
Clusters a given network based on
agglomerative clustering algorithm very
similar to MCODE, but it uses a modified
vertex weighting strategy and can factor in a
measure of network modularity.
Adjustment of only few parameters are
necessary.
Provides network interface to MiSinkenabled Web sites, including DIP.
Predicts gene regulatory network from
biological annotations and expression data.
Systematically partition the given graph,
and layout and color nodes based on GO
terms.
Assign name to selected nodes, and after
unselection, enables user to re-select the
nodes according to the name.
Imports various data from NCBI database.
Imports various data from NCBI database.
Available as part
of core
Highlights the current node and all its
neighboring nodes and edges when the user
hovers the mouse over it.
Identifies densely connected and biopartite
network modules based on combination of
a unique neighbour-sharing score with
hierarchical agglomerative clustering.
Integrates gene expression data of multiple
tissues (ex. from Symatlas) into pre-loaded
network. genes showing characteristic
expression in specified tissues can be
filtered and colored.
Visualizes interaction network on circular
genome. Original GUI with some network
analysis functions (shortest path, degree
distribution, etc.) are equipped.
Finds user defined network motifs in a given
network. network motif can be created and
edited using original GUI.
Computes basic properties of whole
Available as part
network (degree distribution, clustering
of core
coefficients, centrality, etc.)
Allows interactive comparative analysis of
networks across different species.
Paints bar, line or pie graphs onto nodes.
Integrates omics data such as expression
data, proteome data, etc. onto the network
to visualize such data by graph on the
network.
OrthoNets
PanGIA
PathExplorer
Pathintegrator
Pathway Scoring Application
PEPPER
PerturbationAnalyzer
PhosphositePlus Web Service
Client Module
PhyloTree
PICRClient
PINA4MS
PiNGO
PinnacleZ
PSICQUICUniversalClient
PythonScriptingEngine
Randomnetworks
RDFScsape
Enables simultaneous comparison of
interaction network of two species. Protein
domain information can be visualized.
Performs integrated analysis and
visualization of PPIs and genetic interactions
to infer functional modules and interactions
that connect these modules.
Finds paths, filters them based on node
and edge attributes and saves them.
Integrates pathways in which given proteins
are associated.
Evaluates the biological activity of genes
and processes in pathways
Find meaningful pathways / complexes
connecting a protein set members within a
PPI-network using multi-objective
optimization.
Evaluates how perturbation of selected
nodes affect other nodes in a given network
based on level of each node (ex. protein
abundances) and law of mass action.
Integrates phosphorylation-related
information into the network.
Reads a file in phylogenetic tree format
(Phylip or phyloXML) and visualizes it as a
network.
A visualization and analysis tool to study
interactions between multiple sets of
proteins.
Finds candidate genes in a network that are
associated with user-defined target GO
terms.
Searches for subnetworks which can
discriminate givein conditions according to
PPI network and gene expression data
obtained in given conditions
Retrieves interactions associated with
input IDs from databases having PSICQUIC
implementation
Provides Python API.
Generates random network or randomizes
already loaded network.
Allows to query, visualize and reason on
ontologies represented in OWL or RDF
within Cytoscape.
Available in App
Store
Available in App
Store
Available in App
Store
Available in App
Store
Available as part
of core
Reactome FI Plugin
Accesses to Reactome Functional
interaction (FI) network to perform
pathway analyses such as identification of
pathways enriched with proteins in given
network.
ReConn
Communicates with reactome server to load
pathway data onto Cytoscape. Additional
features such as integration of expression
data are supported.
RemainingDegreeDistribution Calculates remaining degree (excess degree)
distribution.
Rene
Allows users to enhance standard
KEGG/Reactome pathways with
information regarding: Transcription
Factors, Proteins and MicroRNAs
ReOrientPlugin
Layouts node positions according to
reference Cytoscape session file.
RubyScriptingEngine
Provides Ruby Script API.
ScriptEngineManager
Manages scripting engines for Cytoscape.
Supports Ruby, JavaScript, Groovy, and
Python.
SemScape
Visualizes Semantic Data Landscapes
SessionForWeb
SetsApp
SFLDLoader
ShortestPath
SimTrek
StringWSClient
structureViz
Superpathways-Plugin
TransClust
Variation
Venn and Euler Diagrams
Saves Cytoscape session in Web format.
Allows the user to create and manipulate
sets of nodes or edges
Represents structural protein families and
their homologs by graph on Cytoscape.
Finds shortest pathway between two
selected nodes.
Assesses similarity of gene ontologies for
given genes and their neighbours. All files
must be installed in plugin folder.
Retrieves interactions associated with input
protein name.
Enables user to traverse from biological
networks to detailed view of their
structures.
Downloads and integrates multiple
pathways from Wikipathways.
Clusters a given similarity graph.
Integrates variation and variation
consequence data on biological networks
Provides a diagram view and a details view
for comparing two or more Cytoscape
groups at a time.
Available in App
Store
Available in App
Store
Available as part
of core
Available in App
Store
Available in App
Store
In Progress
Available in App
Store
Available in App
Store
VistaClaraPlugin
WikiPathways
WordCloud
WormPlot
Provides effective visualization and
analysis platform to analyse expression
data on a given network.
WikiPathways web service client and GPML
file format importer.
Summarizes functions of interacting clusters
as logos, where sizes of logo represents
frequencies of these functions.
V3.1.1
Available in App
Store
Available in App
Store
9. Support Offering Table
Feature
Cytoscape Google
Groups
Helpdesk
Discuss
User Manual
Installation Guide
Tutorials
Presentation Slides
on Web Site
Code Snippets
Purpose
Community
response on best
effort basis
Beneficiary
All users
Comprehensive
manual
Cytoscape
installation
All users
Streamlined
productivity
Enable casual
learning
Commonly used
App development
code
All users
New/Casual
users
All users
App
Developers
URL
mailto:[email protected]
mailto:cytoscape-discuss
@googlegroups.com
http://wiki.cytoscape.org/Cytoscape_3
/UserManual
Section 3 of
http://wiki.cytoscape.org/Cytoscape_3
/UserManual
http://opentutorials.cgl.ucsf.edu/inde
x.php/Portal:Cytoscape3
https://speakerdeck.com/cytoscape
http://wiki.cytoscape.org/Cytoscape_3
/AppDeveloper/Cytoscape_3_App_Co
okbook
10. Future Plans Table
Feature
R/Mathlab/Python
integration
Fast preset network loads
Publish layouts to web
Fast network merge
Large network handling
Java 8 Support
Faster startup times
Nodes displayed as charts
Movies
Additional Visualizations
Additional Analytics
Wallpaper Collection
Case Studies
Cytoscape Clinics
New/Casual User
Power User
App Developer
Purpose
Enable model access,
analysis, and
visualization from
popular tools
Improve load times
leading to quicker
analysis
Enable web users to
view and interact with
networks via browser
Reduce delays when
merging large networks
Improved layout,
interactive, and load
performance
Allow Cytoscape to run
with JVM 8
Reduce delay to get to
initial Welcome screen
Enable users to visualize
nodes as value-sensitive
complex graphics
Clear and interactive
engagement
Publicize good results
associated with
Cytoscape
Streamlined
productivity
Chat rooms give instant
response based on
community availability
Beneficiary
Power users
Timeframe
Fall 2014
New/Casual users
Fall 2014
All users
Fall 2014
All users
Fall 2014
Power users
Fall 2014
All users
Fall 2014
All users
Fall 2014
Power users
Fall 2014
New/Casual users
TBD
All users, potential
users, general public
TBD
TBD
TBD
New/Casual Users
TBD
All users
TBD
11. Issues Addressed
The following issues were addressed in v3.1.1. Details for each issue can be found at Cytoscape’s
RedMine issue repository:
http://code.cytoscape.org/redmine
Issue
521
1541
1841
1875
1979
2041
2050
2055
2066
2185
2334
2429
2438
2465
2470
2475
2497
2501
2504
2510
2511
2512
2514
2516
2520
2537
2548
2556
2559
2560
2563
2564
Description
Port KGMLReader
Cytoscape 3.x <-> Cytoscape.js integration (import/export and app
deployment to web)
Implement a JSON I/O bundle
Design formats for JSON I/O Module
Edge handles recreated
Tasks returned by createTaskIterator(File) in TaskFactories abort with
NPE
Can save a big network but cannot reload it
JVM SIGSEGV appears on Cytoscape startup/shutdown on Ubuntu
13.04+Oracle Java 7
Import network from MS Excel
Enable Compiling Without An Internet Connection
CyNetworkViewDesktopMgr.setBounds() Fails for Maximized Internal
Frames
Can't import List columns from exported table
Import Ontology/Annotation table preview doesn't use column colors
shown in legend
JDialogTaskManager/CyTableImpl threw: column already exists ...
'layoutAlgorithm'
Circular Layout Progress Stalled
Event chain can be disrupted by a listener that throws an exception
Undo Cut Nodes/Edges does not restore bypass values
Redo:Cut throws NullPointerException and does not work
Edge attributes don't apply to subsequently imported sif files
containing same edge IDs
Cytoscape freezes on Mac Java 7 when importing multiple networks
using keyboard shortcuts
Mappings sometimes not applied when restoring session
KEGG XML
Session saved with equation return type not matching column type
results in instability when reloaded
Filters not cleared when starting/loading new session
Filters not restored properly when opening saved session with
modified default filter
Merge networks hangs
ConcurrentModificationException When Recreating CyNetworkViews
Enable CytoscapeConfiguration to exist in a settable location
Collapsed groups are not properly restored from sessions
Edge-weighted Spring Embedded spring strength setting not having
any effect
Topology filter changed behavior in v3.1 relative to v3.0
Can't search based on Integer column values
Beneficiary
All Users
All Users
All Users
All Users
All Users
All Users
Power Users
All Users
All Users
Developers
All Users
All Users
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All Users
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Power Users
Power Users
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2565
2575
2576
2579
2586
2587
2593
2609
2613
2617
2637
2639
2642
2653
Legacy Node Attributes Format Should Support Lists of Strings
Nested filters can't be deserialized
Initial state of column filter has null criterion
Filters no longer support boolean columns
Ding deadlock in 3.1.1
Network import file command does not work for .txt and .csv files
Table importing/attribute mapping dialog malformed and fails for
certain networks
Cytoscape.js JSON reader does not read network table
Node (x,y) positions are ignored in 3.1.0
Slider interval should always be visible/editable
"Mapping Column for New Network" (sourceColumnList) Tunable
exists in GUI, but is never used
Cytoscape group not behaving as expected
"Mapping Column for Existing Network" tunable has
unwieldy/confusing name
Command processing using "-S" is broken
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All Users
Developers
Power Users
Developers
Power Users